From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sun May 10 2009 - 21:29:32 CDT
Hi Jerome, Hi Chris Chipot,
@Chris Chipot: I think including Jerome's pic that I got through the
link from Chris Harrison should definitely help.
@Jerome:
ok, the lambda=1 case is fine with me :-)
however, for the lambda=0 case:
> Lennard-Jones (and of course it goes to zero as lambda vanishes). So
This is right for lambda_up_LJ, but what about lambda_down_LJ at lambda=0?
a) is there simply no soft-core potential for the vanishing set of
particles?
b) the vanishing set of particles are not expected to have clashes
if a): @Chris: maybe one could stress explicitly what interactions (what
with what) are considered for the soft-core potentials?
if b): is "fepVdwShiftCoeff=5.0" a little high, considering that even
non-clashing particles have distances of 3A or so?
Sorry, I lost the link to your original soft-core paper, if you could
send it to me again?
Thank you,
Sebastian
Jerome Henin wrote:
> Hi Sebastian,
>
> There is no need to neglect anything, the soft-core formalism is
> analytically accurate. Have a look at the expression for the soft-core
> potential and let lambda be 1: then it becomes identical to a 6-12
> Lennard-Jones (and of course it goes to zero as lambda vanishes). So
> switching from L-J to soft-core only changes the intermediate states 0
> < lambda < 1, not the end-points of the calculation, hence it does not
> change the (converged) free energy difference.
>
> Best,
> Jerome
>
> On Sun, May 10, 2009 at 11:36 AM, Sebastian Stolzenberg
> <s.stolzenberg_at_gmail.com> wrote:
>
>> Thank you, Chris, I missed that link,
>>
>> theres is one more thing attracting my curiosity, the vdW
>> hard-core<->soft-core transitions:
>>
>> The real vdW potential is hard-core, but NAMD2.7b FEP can use soft-core.
>> Can one really neglect \delta_G from a hard-core<->soft-core transition?
>> How could one measure \delta_G and thus convince oneself in practice?
>>
>> Thank you,
>> Best,
>> Sebastian
>>
>>
>> Chris Harrison wrote:
>>
>>> Sebastion,
>>>
>>> Please look here to begin:
>>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9953.html
>>>
>>>
>>>
>>> C.
>>>
>>>
>>> --
>>> Chris Harrison, Ph.D.
>>> Theoretical and Computational Biophysics Group
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>>>
>>> char_at_ks.uiuc.edu <mailto:char_at_ks.uiuc.edu>
>>> Voice: 217-244-1733
>>> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
>>> Fax: 217-244-6078
>>>
>>>
>>>
>>> On Fri, May 8, 2009 at 11:57 AM, Sebastian Stolzenberg
>>> <s.stolzenberg_at_gmail.com <mailto:s.stolzenberg_at_gmail.com>> wrote:
>>>
>>> Dear All,
>>>
>>> I have some trouble interpreting the new parameters (listed below)
>>> in the namd 2.7b manual's FEP chapter.
>>> Here are my interpretations, I would be glad if you could check
>>> them with me:
>>>
>>> I assume that decouple is set to "on".
>>>
>>> manual p. 118:
>>> "fepVdwShiftCoeff / tiVdwShiftCoeff":
>>> considered are only vdW interactions between the growing/shrinking
>>> particles and their respective environments only.
>>> (otherwise: what's the use of soft-core for vdW of the environment
>>> with itself?)
>>>
>>> "fepElecLambdaStart/tiElecLambdaStart ":
>>> considered are only the elect. interactions of the growing
>>> particles with its environment:
>>> E_el(0.5)=0 linearly increased to E_el(1.0)=full strength
>>> (my thinking is that interactions between the shrinking particles
>>> with the environment are *decreasing*)
>>>
>>> p. 119:
>>> "fepVdwLambdaEnd / tiVdwLambdaEnd":
>>> it means that @lambda>0.5, we set fepVdwShiftCoeff
>>> (tiVdwShiftCoeff) to zero.
>>>
>>> Is this all correct?
>>> If yes, then @lambda=0, I see an abrupt transition from
>>> "hard-core" to "soft-core" for vdW interactions between shrinking
>>> particles and their environment.
>>> Is the corresponding free energy difference negligible with the
>>> default fepVdwShiftCoeff value of 5A^2? If not, how can one
>>> practically measure this free energy difference?
>>>
>>> Thank you,
>>> Best,
>>> Sebastian
>>>
>>>
>>>
>>
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